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<title>Per Base Sequence Quality</title>
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<h1>Per Base Sequence Quality</h1>
<h2>Summary</h2>
<p>
This view shows an overview of the range of quality values across all bases
at each position in the FastQ file.
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<p><img src="per_base_quality.png"></p>
<p>
For each position a BoxWhisker type plot is drawn.  The elements of the
plot are as follows:
</p>
<ul>
<li>The central red line is the median value</li>
<li>The yellow box represents the inter-quartile range (25-75%)</li>
<li>The upper and lower whiskers represent the 10% and 90% points</li>
<li>The blue line represents the mean quality</li>
</ul>
<p>
The y-axis on the graph shows the quality scores.  The higher the score
the better the base call.  The background of the graph divides the 
y axis into very good quality calls (green), calls of reasonable quality
(orange), and calls of poor quality (red).  The quality of calls on most
platforms will degrade as the run progresses, so it is common to see
base calls falling into the orange area towards the end of a read.
</p>
<p>
It should be mentioned that there are number of different ways to encode
a quality score in a FastQ file.  FastQC attempts to automatically determine
which encoding method was used, but in some very limited datasets it is
possible that it will guess this incorrectly (ironically only when your
data is universally very good!).  The title of the graph will describe the
encoding FastQC thinks your file used.
</p>


<h2>Warning</h2>
<p>
A warning will be issued if the lower quartile for any base is less
than 10, or if the median for any base is less than 25.
</p>

<h2>Failure</h2>
<p>
This module will raise a failure if the lower quartile for any base is
less than 5 or if the median for any base is less than 20.
</p>

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